Lineage for Family d.58.7.1: Canonical RBD

  1. Root: SCOPe 2.08
  2. Class d: Alpha and beta proteins (a+b) [53931] (396 folds)
  3. Fold d.58: Ferredoxin-like [54861] (62 superfamilies)
    alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
  4. Superfamily d.58.7: RNA-binding domain, RBD, aka RNA recognition motif (RRM) [54928] (6 families) (S)
  5. Family d.58.7.1: Canonical RBD [54929] (70 proteins)
    Pfam PF00076
    Pfam PF13893

Proteins:

  1. Alkylation repair AlkB homolog 8, ALKBH8 [143334] (1 species)
  2. APOBEC1 stimulating protein [143326] (1 species)
  3. Arginine/serine-rich splicing factor 10 [143312] (1 species)
  4. Ataxin-2-binding protein 1 [143292] (1 species)
  5. Calcipressin-1 [117953] (1 species)
  6. CBP20, 20KDa nuclear cap-binding protein [64274] (1 species)
  7. Cleavage stimulation factor, 64 kda subunit [102983] (1 species)
  8. Cold-inducible RNA-binding protein [143300] (1 species)
  9. CUG triplet repeat RNA-binding protein 1 [143336] (1 species)
  10. E3 ubiquitin protein ligase CNOT4 [143294] (1 species)
    CCR4-NOT transcription complex subunit 4
  11. Eukaryotic translation initiation factor 3 subunit 4 [143304] (1 species)
  12. Eukaryotic translation initiation factor 4B [117973] (1 species)
  13. Heterogeneous nuclear ribonucleoprotein d0 [54944] (1 species)
  14. Heterogeneous nuclear ribonucleoprotein H' [117955] (1 species)
  15. Heterogeneous nuclear ribonucleoprotein L-like [117951] (1 species)
  16. Heterogeneous nuclear ribonucleoproteins A2/B1 [143342] (1 species)
  17. Heterogeneous nuclear ribonucleoproteins C1/C2 [117961] (1 species)
  18. HIV Tat-specific factor 1 [143290] (1 species)
  19. Hu antigen C (Huc) [54940] (1 species)
  20. Hu antigen D (Hud) [54942] (1 species)
  21. Hypothetical protein FLJ20273 [143328] (1 species)
  22. IGF-II mRNA-binding protein 2 isoform A [143344] (1 species)
  23. Limkain-b1, LKAP [143324] (1 species)
    KIAA0430
  24. Lupus LA protein [89940] (1 species)
  25. Matrin 3 [143306] (1 species)
  26. Musashi-1 [102981] (1 species)
  27. Negative elongation factor E, NELF-E [143302] (1 species)
  28. Neural RNA-binding protein Musashi-1 [54946] (1 species)
  29. Non-POU domain-containing octamer-binding protein, NonO [143354] (1 species)
  30. Nuclear factor Aly [102979] (1 species)
  31. Nuclear ribonucleoprotein A1 (RNP A1, UP1) [54930] (1 species)
    duplication: contains two domains of this fold
  32. Nuclear ribonucleoprotein D0 (AUF1) [75439] (1 species)
  33. Nucleolin [54952] (2 species)
    1. Species Golden hamster (Mesocricetus auratus) [TaxId:10036] [54953] (4 PDB entries)
    2. Species Human (Homo sapiens) [TaxId:9606] [255371] (1 PDB entry)
  34. Nucleolysin TIAR [143298] (1 species)
  35. Nucleoporin 35 [143330] (1 species)
  36. Peptidyl-prolyl cis-trans isomerase E, N-terminal domain [143310] (1 species)
  37. Poly(A)-binding protein [54948] (1 species)
  38. Poly(A)-specific ribonuclease PARN [117967] (1 species)
  39. Polypyrimidine tract-binding protein [54950] (1 species)
  40. Polypyrimidine tract-binding protein 2, PTBP2 [143332] (1 species)
  41. Pre-mRNA branch site protein p14 [143316] (1 species)
  42. Pre-mRNA splicing factor Cwc2 / Cwf2 / Prp3, RRM domain [346093] (2 species)
    1. Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:559292] [346356] (3 PDB entries)
    2. Species Schizosaccharomyces pombe 972h- [TaxId:284812] [346357] (1 PDB entry)
  43. Pre-mRNA splicing factor Cwf5 / Ecm2 / Stl11, RRM domain [346094] (1 species)
    3jb9 a:178-285 is Cwf5 RRM from fission yeast; not included because sids are not case sensitive
  44. Probable RNA-binding protein 19, Rbm19 [117969] (1 species)
  45. Probable RNA-binding protein KIAA1579 [117963] (1 species)
  46. Putative RNA-binding protein 15B, Rbm15b [117971] (1 species)
  47. Ribonucleoprotein PTB-binding 1, Raver-1 [143308] (1 species)
  48. RNA binding protein 23 [143352] (1 species)
  49. RNA-binding motif, single-stranded-interacting protein 1, RBMS1 [143356] (1 species)
  50. RNA-binding motif, single-stranded-interacting protein 2, RBMS2 [143320] (1 species)
  51. RNA-binding protein 12 [143349] (2 species)
    3rd RBD
    1. Species Human (Homo sapiens) [TaxId:9606] [143350] (3 PDB entries)
      Uniprot Q9NTZ6 412-523! Uniprot Q9NTZ6 536-638
    2. Species Mouse (Mus musculus) [TaxId:10090] [143351] (1 PDB entry)
      Uniprot Q8R4X3 917-1002
  52. RNA-binding protein 28 [143358] (1 species)
  53. RNA-binding protein 41, RBM41 [143296] (1 species)
  54. RNA-binding protein 8 [89938] (2 species)
    1. Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [89939] (3 PDB entries)
      CG8781 protein
    2. Species Human (Homo sapiens) [TaxId:9606] [102978] (3 PDB entries)
      RBM8A, Y14
  55. RNA-binding protein 9 [143314] (1 species)
  56. RNA-binding protein EWS [143340] (1 species)
  57. RNA-binding protein Raly (Autoantigen p542) [117959] (1 species)
  58. RNA-binding protein UBP1 [143322] (1 species)
  59. RNA-binding region containing protein 1 [143360] (1 species)
  60. Sex-lethal protein [54938] (1 species)
  61. Spliceosomal U2 small nuclear ribonucleoprotein B' / U2B' / Msl1 protein [54934] (2 species)
    3jb9 chain k is Msl1 from fission yeast; not included because sids are not case sensitive
    1. Species Human (Homo sapiens) [TaxId:9606] [54935] (1 PDB entry)
    2. Species Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292] [346359] (1 PDB entry)
  62. Splicesomal U1A protein [54932] (2 species)
    duplication: contains two domains of this fold
    1. Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [160313] (3 PDB entries)
      Uniprot P43332 1-104! Uniprot P43332 134-216
    2. Species Human (Homo sapiens) [TaxId:9606] [54933] (54 PDB entries)
      Uniprot P09012 1-97 ! Uniprot P09012 4-98 ! Uniprot P09012 1-98
  63. Splicing factor 3B subunit 4 [143318] (1 species)
  64. Splicing factor U2AF 65 KDa subunit [54936] (2 species)
    1. Species Human (Homo sapiens) [TaxId:9606] [54937] (10 PDB entries)
    2. Species Mouse (Mus musculus) [TaxId:10090] [256391] (2 PDB entries)
  65. Splicing factor, arginine/serine-rich 1, SFRS1 [143346] (2 species)
    1. Species Human (Homo sapiens) [TaxId:9606] [143347] (3 PDB entries)
      Uniprot Q07955 1-95
    2. Species Mouse (Mus musculus) [TaxId:10090] [143348] (1 PDB entry)
      Uniprot Q6PDM2 112-206
  66. Splicing factor, arginine/serine-rich 9 (SFRS9) [117965] (1 species)
  67. Synaptojanin 2 [102985] (1 species)
  68. TAR DNA-binding protein 43, TDP-43 [117957] (1 species)
  69. U4/U6 snRNA-associated-splicing factor PRP24 [143338] (1 species)
    contains three RBDs
  70. automated matches [190332] (5 species)
    not a true protein
    1. Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [311207] (3 PDB entries)
    2. Species Human (Homo sapiens) [TaxId:9606] [187155] (29 PDB entries)
    3. Species Mouse (Mus musculus) [TaxId:10090] [188825] (3 PDB entries)
    4. Species Nematode (Caenorhabditis elegans) [TaxId:6239] [258944] (3 PDB entries)
    5. Species Norway rat (Rattus norvegicus) [TaxId:10116] [272203] (1 PDB entry)

More info for Family d.58.7.1: Canonical RBD

Timeline for Family d.58.7.1: Canonical RBD: